If you boot the Ipod with the Apple firmware no Rockbox code is running. If Itunes doesn't recognize it in that case you have a problem with the Ipod, and no problem Rockbox can do anything about.
AFAIk Itunes doesn't recognize an Ipod in Rockbox USB mode simply because the Apple firmware has some vendor specific extensions to the SCSI protocol that Rockbox doesn't support. It should still recognize it as removeable drive though.